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Two upland cotton tree fiber samples from different seasons

ABSTRACT: Two fiber tissues harvested 10 days post anthesis from upland cotton trees grown under the same green house conditions except for different seasons of the year were used for RNA extraction. Small RNA molecules under 30 bases were amplified and isolated from an agarose gel. The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina Genome Analyzer according to the manufacturer's instructions. The 35nt sequence tags from sequencing went through data cleaning first, which included getting rid of the low-quality tags and several kinds of contaminants from the 35nt tags. All clean tag sequences with copy numbers were then summarized into a fasta format file.

ORGANISM(S): Gossypium hirsutum

PROVIDER: GSE27697 | GEO | 2011/07/01

SECONDARY ACCESSION(S): PRJNA138137

REPOSITORIES: GEO

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Two upland cotton tree fiber samples from different seasons

Project description:Two fiber tissues harvested 10 days post anthesis from upland cotton trees grown under the same green house conditions except for different seasons of the year were used for RNA extraction. Small RNA molecules under 30 bases were amplified and isolated from an agarose gel. The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina Genome Analyzer according to the manufacturer's instructions. The 35nt sequence tags from sequencing went through data cleaning first, which included getting rid of the low-quality tags and several kinds of contaminants from the 35nt tags. All clean tag sequences with copy numbers were then summarized into a fasta format file. Fiber samples from different seasons were used for small RNA sequencing and data processing.

2011-07-01 | E-GEOD-27697 | biostudies-arrayexpress

non-coding RNA sequencing of upland cotton fiber and ovule

Project description:Three samples of cotton fiber harvested 3, 7 and 15 days post anthesis (DPA) and a sample of cotton ovule harvestd 0 DPA were used for non-coding RNA extraction and seloxa sequencing experiments, respectively.Cotton plants (Gossypium hirsutum cv. Xuzhou 142) were grown in a soil mixture in fully automated walk-in growth rooms with 300 µmol m–2 s–1 average light intensity, 60% relative humidity and temperatures set to 30C during the light period and 28C during the dark (12-h light/dark cycle). These conditions were consistent throughout the year. Small RNA molecules under 30 bases were amplified and isolated from an agarose gel. The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina Genome Analyzer IIx according to the manufacturer's instructions. The 38nt sequence tags from sequencing went through data cleaning first, which included getting rid of the low-quality tags and clipping adapter sequences.

2012-06-06 | GSE37125 | GEO

non-coding RNA sequencing of upland cotton fiber and ovule

Project description:Three samples of cotton fiber harvested 3, 7 and 15 days post anthesis (DPA) and a sample of cotton ovule harvestd 0 DPA were used for non-coding RNA extraction and seloxa sequencing experiments, respectively.Cotton plants (Gossypium hirsutum cv. Xuzhou 142) were grown in a soil mixture in fully automated walk-in growth rooms with 300 M-BM-5mol mM-bM-^@M-^S2 sM-bM-^@M-^S1 average light intensity, 60% relative humidity and temperatures set to 30C during the light period and 28C during the dark (12-h light/dark cycle). These conditions were consistent throughout the year. Small RNA molecules under 30 bases were amplified and isolated from an agarose gel. The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina Genome Analyzer IIx according to the manufacturer's instructions. The 38nt sequence tags from sequencing went through data cleaning first, which included getting rid of the low-quality tags and clipping adapter sequences. Three samples of cotton fiber harvested 3, 7 and 15 days post anthesis (DPA) and a sample of cotton ovule harvestd 0 DPA were used for non-coding RNA extraction and seloxa sequencing experiments, respectively.

2012-06-06 | E-GEOD-37125 | biostudies-arrayexpress

upland soil

Project description:upland soil Metagenome

| PRJNA437209 | ENA

cDNA expression profiles of +7 DPA wild-type upland cotton (Gossypium hirsutum cv. Xuzhou142) ovules over the one-year cycle

Project description:A cDNA library from 0-10 day post anthesis cotton ovules was established to study genes expressed in cotton ovule during initiation and quickly elongation period. We randomly sequenced over 100,000 ESTs from this library and acquired a gene pool of more than 28,000 UniESTs. The cotton UniESTs were then PCR-amplified and printed onto microarray. This array is comprised of about 28000 high-quality cotton cDNAs (with average length>750bp) and external controls. To study the different growth potential of cotton fibers in a one-year cycle, we then hybridized the array with RNA samples derived from +7 DPA wild-type upland cotton fibers in four different seasons, respectively.

2010-06-01 | GSE16802 | GEO

red upland soil

Project description:red upland soil Assembly

| PRJNA553863 | ENA

Comparison of the Global Gene Expression Profiles in the Bovine Endometrium between Summer and Autumn Seasons

Project description:To examine the difference of the endometrial conditions in the cows between on summer and autumn seasons, gene expression profiles were compared. The expressions of 268 genes were significantly higher in the endometrium collected on summer than those on autumn, whereas 369 genes were lower (P<0.05 or lower). Transcripts of GP2 and NTS were more abundant in the endometrium of summer than those of autumn (P<0.05). In contrast, the mRNA expressions of CDH1 and HSPH1 were lower in the endometrium of summer seasons (P<0.1). Collectively, the different gene expression profiles may contribute to functional differences of endometrium between the summer and autumn seasons, and GP2 and NTS may have a relevance to endometrial deficiency that cause infertility of cows on summer seasons.

2015-02-19 | GSE66057 | GEO

cDNA array expression profile of wild-type and fl-mutant upland cotton ovules

Project description:Comparison of gene expression profiles of wild-type and fl-mutant upland cotton ovules Keywords: repeat samples

2006-01-01 | GSE2901 | GEO

Rice gene expression in irrigated and rainfed fields during two seasons

Project description:To identify the concurrent effects of multiple environmental factors on gene expression under natural climatic fluctuations in rice, we examined global gene expression patterns in two fields typical of the main modes of rice cultivation, over two seasons, each comprising 15 time-points in three different genotypes

2015-10-01 | GSE73609 | GEO

Melospiza melodia hypothalamus: control and STI in two seasons (spring and autumn)

Project description:Male song sparrows (Melospiza melodia) are territorial year-round; however, neuroendocrine responses to simulated territorial intrusion (STI) differ between breeding (spring) and non-breeding seasons (autumn). In spring, exposure to STI leads to increases in luteinizing hormone and testosterone, but not in autumn. These observations suggest that there are fundamental differences in the mechanisms driving neuroendocrine responses to STI between seasons. Microarrays, spotted with EST cDNA clones of zebra finch, were used to explore gene expression profiles in the hypothalamus after territorial aggression in two different seasons. Free-living territorial male song sparrows were exposed to either conspecific or heterospecific (control) males in an STI in spring and autumn. Behavioral data were recorded, whole hypothalami were collected, and microarray hybridizations were performed. Quantitative PCR was performed for validation. Our results show 262 cDNAs were differentially expressed between spring and autumn in the control birds. There were 173 cDNAs significantly affected by STI in autumn; however, only 67 were significantly affected by STI in spring. There were 88 cDNAs that showed significant interactions in both season and STI. Results suggest that STI drives differential genomic responses in the hypothalamus in the spring vs. autumn. The number of cDNAs differentially expressed in relation to season was greater than in relation to social interactions, suggesting major underlying seasonal effects in the hypothalamus which may determine the differential response upon social interaction. Functional pathway analyses implicated genes that regulate thyroid hormone action and neuroplasticity as targets of this neuroendocrine regulation.

2009-12-16 | GSE18970 | GEO

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